How to join group objects into one
If you just want to organize them conveniently, you can simply group them into a new group (or several, if needed). To select all objects within a group, first, switch the Outliner's Type display mode to Groups, then click on the icon(s):



If you want to remove them out of those empties, you can press Shift Ctrl A to make all selected duplicates real, instead of instancing: